Department of Botany and Plant Pathologyhttp://hdl.handle.net/1957/1932
Tue, 24 Mar 2015 16:31:35 GMT2015-03-24T16:31:35ZDurable resistance: A key to sustainable management of pathogens and pestshttp://hdl.handle.net/1957/55366
Durable resistance: A key to sustainable management of pathogens and pests
Mundt, Christopher C.
This review briefly addresses what has been learned about resistance durability in recent years, as well as
the questions that still remain. Molecular analyses of major gene interactions have potential to contribute
to both breeding for resistance and improved understanding of virulence impacts on pathogen fitness.
Though the molecular basis of quantitative resistance is less clear, substantial evidence has accumulated
for the relative simplicity of inheritance. There is increasing evidence for specific interactions with quantitative
resistance, though implications of this for durability are still unknown. Mechanisms by which
resistance gene pyramids contribute to durability remain elusive, though ideas have been generated
for identifying gene combinations that may be more durable. Though cultivar mixtures and related
approaches have been used successfully, identifying the diseases and conditions that are most conducive
to the use of diversity has been surprisingly difficult, and the selective influence of diversity on pathogen
populations is complex. The importance of considering resistance durability in a landscape context has
received increasing emphasis and is an important future area of research. Experimental systems are being
developed to test resistance gene deployment strategies that previously could be addressed only with
logic and observation. The value of molecular markers for identifying and pyramiding major genes is
quite clear, but the successful use of quantitative trait loci (QTL) for marker-assisted selection of quantitative
resistance will depend greatly on the degree to which the identified QTL are expressed in different
genetic backgrounds. Transgenic approaches will likely provide opportunities for control of some recalcitrant
pathogens, though issues of durability for transgenes are likely to be no different than other genes
for resistance. The need for high quality phenotypic analysis and screening methodologies is a priority,
and field-based studies are likely to remain of signal importance in the foreseeable future.
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Elsevier. The published article can be found at: http://www.journals.elsevier.com/infection-genetics-and-evolution.
Wed, 01 Oct 2014 00:00:00 GMThttp://hdl.handle.net/1957/553662014-10-01T00:00:00ZFinding Our Way through Phenotypeshttp://hdl.handle.net/1957/55349
Finding Our Way through Phenotypes
Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva; Cooper, Laurel D.; Jaiswal, Pankaj; et al.
Despite a large and
multifaceted effort to understand
the vast landscape of phenotypic
data, their current form inhibits
productive data analysis. The lack
of a community-wide, consensus-based,
human- and machine-interpretable
language for describing
phenotypes and their genomic and
environmental contexts is perhaps
the most pressing scientific bottleneck
to integration across many
key fields in biology, including
genomics, systems biology, development,
medicine, evolution, ecology,
and systematics. Here we
survey the current phenomics landscape,
including data resources and
handling, and the progress that has
been made to accurately capture
relevant data descriptions for phenotypes.
We present an example of
the kind of integration across
domains that computable phenotypes
would enable, and we call
upon the broader biology community,
publishers, and relevant funding
agencies to support efforts to
surmount today’s data barriers and
facilitate analytical reproducibility.
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://journals.plos.org/plosbiology/.
Tue, 06 Jan 2015 00:00:00 GMThttp://hdl.handle.net/1957/553492015-01-06T00:00:00ZA new model to simulate climate-change impacts on forest succession for local land managementhttp://hdl.handle.net/1957/55282
A new model to simulate climate-change impacts on forest succession for local land management
Yospin, Gabriel I.; Bridgham, Scott D.; Neilson, Ronald P.; Bolte, John P.; et al.
We developed a new climate-sensitive vegetation state-and-transition simulation
model (CV-STSM) to simulate future vegetation at a fine spatial grain commensurate
with the scales of human land-use decisions, and under the joint influences of changing
climate, site productivity, and disturbance. CV-STSM integrates outputs from four different
modeling systems. Successional changes in tree species composition and stand structure were
represented as transition probabilities and organized into a state-and-transition simulation
model. States were characterized based on assessments of both current vegetation and of
projected future vegetation from a dynamic global vegetation model (DGVM). State
definitions included sufficient detail to support the integration of CV-STSM with an agent-based
model of land-use decisions and a mechanistic model of fire behavior and spread.
Transition probabilities were parameterized using output from a stand biometric model run
across a wide range of site productivities. Biogeographic and biogeochemical projections from
the DGVM were used to adjust the transition probabilities to account for the impacts of
climate change on site productivity and potential vegetation type. We conducted experimental
simulations in the Willamette Valley, Oregon, USA. Our simulation landscape incorporated
detailed new assessments of critically imperiled Oregon white oak (Quercus garryana) savanna
and prairie habitats among the suite of existing and future vegetation types. The experimental
design fully crossed four future climate scenarios with three disturbance scenarios. CV-STSM
showed strong interactions between climate and disturbance scenarios. All disturbance
scenarios increased the abundance of oak savanna habitat, but an interaction between the
most intense disturbance and climate-change scenarios also increased the abundance of
subtropical tree species. Even so, subtropical tree species were far less abundant at the end of
simulations in CV-STSM than in the dynamic global vegetation model simulations. Our
results indicate that dynamic global vegetation models may overestimate future rates of
vegetation change, especially in the absence of stand-replacing disturbances. Modeling tools
such as CV-STSM that simulate rates and direction of vegetation change affected by
interactions and feedbacks between climate and land-use change can help policy makers, land
managers, and society as a whole develop effective plans to adapt to rapidly changing climate.
To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The published article is copyrighted by the Ecological Society of America and can be found at: http://www.esajournals.org/loi/ecap.
Thu, 01 Jan 2015 00:00:00 GMThttp://hdl.handle.net/1957/552822015-01-01T00:00:00ZPathogenicity, Fungicide Resistance, and Genetic Variability of Phytophthora rubi Isolates from Raspberry (Rubus idaeus) in the Western United Stateshttp://hdl.handle.net/1957/55262
Pathogenicity, Fungicide Resistance, and Genetic Variability of Phytophthora rubi Isolates from Raspberry (Rubus idaeus) in the Western United States
Stewart, Jane E.; Kroese, Duncan; Tabima, Javier F.; Larsen, Meredith M.; Fieland, Valerie J.; Press, Caroline M.; Zasada, Inga A.; Grünwald, Niklaus J.
Root rot of raspberry (Rubus idaeus), thought to be primarily caused
by Phytophthora rubi, is an economically important disease in the
western United States. The objectives of this study were to determine
which Phytophthora species are involved in root rot, examine the efficacy
of different isolation methods (cane, root, and root/soil baiting
with young raspberry plants), and determine if pathogenicity, fungicide
resistance, and/or genetic variation exists among P. rubi isolates collected
from raspberry fields in Washington, Oregon, and California. Of
275 samples, direct isolation from cane material resulted in a greater
number of P. rubi isolates (39%), whereas root/soil baiting yielded the
least (11%). Sequencing of the internal transcribed spacer region of
210 of the total 597 collected Phytophthora isolates showed that all but
one isolate (identified as P. bisheria) were P. rubi. Results of the pathogenicity
and fungicide resistance to mefenoxam comparing 14 total
isolates from Washington, Oregon, and California showed that isolates
were similarly virulent against red raspberry and the EC₅₀ frequency
distributions showed no significant difference. These results, combined
with amplified fragment length polymorphism results show that P. rubi
isolates from Washington, Oregon, and California represent one large
mixed population. This work provides novel insights into the isolation
and biology of P. rubi in western U.S. raspberry production systems.
To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the publisher’s final pdf. The article was published by the American Phytopathological Society and is in the public domain. The published article can be found at: http://apsjournals.apsnet.org/loi/pdis.
Mon, 01 Dec 2014 00:00:00 GMThttp://hdl.handle.net/1957/552622014-12-01T00:00:00Z